Lawrence III begins to detail his plot in his Air Battle Ship of capturing the Beast of the Sea. To accomplish this he must capture all three of the Legendery Birds and disturb their balance of power. To begin his quest, he decides to first capture Moltres by launching below-zero ice balls at its island. Moltres comes out of its' cave in its' island to defend itself, but it only finds peltering ice balls being thrown it. Six Circle rings are shot toward Moltres to capture it. It is able to dodge a few, but is not powerful enough to resist them all. The defensesless Moltres is then pulled into the Air Battle Ship, and the man moves on to capture his second target.

Ash, Misty, and Tracey are continuing their quest to compete in the Orange League. Today, they decided to take a rest. A new character appears, the boat driver, that drives them around in her boat. These surroundings are very relaxing, and Ash has the idea to let all his Pokémon enjoy the day too. Ash, Misty, and Tracey release all their Pokémon onto the boat and in the water. What Ash and the gang don't know is that Team Rocket is attempting to ruin his plans. Team Rocket trails Ash's boat in their mechanical Magikarp. But no worrys, Team Rocket is swept away in a horde of Magikarp.

Suddenly, the sky turns black and clouds roll in. The sea tumbles and throws Ash's boat from side to side. Trying to survive this storm, they notice an island off in the distance. The sea throws them into the bay of the island. Team Rocket, with their consistant, runs into cliff, ruining their Magikarp. Ash's boat crash lands onto the island's rocky beach, which totals the boat. A tribe of cannibals with war paint and wooden masks rush at Ash, Misty, and Tracey as they hop off the boat. the boat driver steps in to resolve the dilemma between Ash and the tribesmen. She gives the natives a hello. One of them, Carol, takes off their mask and talks to the boat driver. The boat driver knows Carol and explains what happen to them on the stormy evening. The boat driver introduces the natives to Ash, Misty, Tracey. Carol explains that she will not be doing the ceremony anymore, but her sister Melody will. The boat driver mentions that Ash is a Pokémon Trainer. One of the older islanders rush towards Ash telling him that he is the chosen one and that he must rechieve the 3 mystic titan balls from the sorrounding islands. Ash is stunned by this and stands in awe. The older cannibal reassures Ash by telling him that tomorrow is the annual celebration for the three Titan Birds, and that every year a Pokémon Trainer is appointed to accomplish the task that Ash has been given. Ash, as usual, jumps up and down getting excited and stuff. The now nice villagers lead Ash and everyone to a feast for the big celebration. While Ash is eating, Melody starts dancing and playing her flute. She hops down off the stage and tells Ash that he must get 3 balls from 3 different islands. Ash, being anxious, agrees and decides to go now into the pitch black. Melody does not support Ash 's idea for he has the next day to do it also. But, Ash insists on going. The boat driver likes Ash's attitude and so she gives him a ride in her boat.

On the way to the first island, the Fire Island, the weather kicks up again and tosses the boat around. After many throws and hurls, they finally get to the island in their crashed boat. Ash hops out of the boat and runs up the ancient ruins to first ball as Pikachu insistenly leads. Back in Pallet town, Professor Oak takes a bike ride to Ash's house where he meets Ash's mom and Mr. Mime who is working. Mr. Mime notices the bad weather approching and brings an umbrella to Ash's Mom, Deelia. The storm continues on and on soaking Oak and Deelia. The weather begins to clear up and colors start flashing in the sky. Many Pokémon also fly north to an unknown random area . Oak contacts Professor Ivy and goes over what is happening with her. The two professor go on the TV News and explain that the source of the bad weather is from the middle of the Orange Islands. They relate this current weather condition to the legend of "Beast of the Sea".

Seeing that the weather has worsened, Melody hops in her sister's boat to go resuce Ash. Misty and Tracey follow, yet they do not want to. Team Rocket, staggering on to the coast, notices that everyone is running to their boat in the horrid weather. Team Rocket hops in Melody's boat and barely hides under a sheet of blankets. Because of the troublsome storm, the sea thrashed about. Team Rocket, only holding onto their blanket, gets launced all the way to the center of the island using the blanket as a parachute. Through many difficulties, Melody, Misty, and Tracey finally get to the island. Expecting the best, their doubts are wearsend when they see the crashed boat of the boat driver. The boat driver tells them that Ash is okay and that he went up the ancient stairway to get the ball.

Melody puts up the sails on her speed boat into a sail boat and glide right up the stairway. They meet Ash at the Small Shrine of Fire Island. Ash removes the Fire Ball. Coincidently, Team Rocket is hidden behind a rock, for they landed there from their launching out of the boat. As Ash pockets the ball, Zapdos flies in, sending electric stroms everywhere. Pikachu sends lighting bolts back at the Zapdos. Zapdos lands on the fire shrine, and Pikachu exchanges electricty bolts with it. Meowth explains that the two Pokémon are talking and tells that Zapdos is saying that since the occurence of Motres's abscence, it now takes Fire Island as its own.

Zapdos begins to launch a big lighting storm, but only finds out that his electricity is being absorbed by the Air Battle Ship. Lawrence III is now planning to capture Zapdos. He weakens it by absorbing it's electricty, but this is only his plan's beginning. Zapdos tries to attack the ship, but is stopped by that attacks of Lawrence III. Square rings come out of the ship and capture Zapdos with ease. Ash, Misty, Tracey, Team Rocket, Melody, and the boat driver are also captured, and thrown into a cage. They are then taken into the ship.

Lawrence III's computer notifies them that it has captured something else besides the Zapdos. Lawrence III goes down to the capture chamber and see's Zapdos, Moltres, and the cage of kids. He releases the kids and says he is going to capture all the three legendery birds to tame the beast of the sea, as it says on the table in front of them. Ash and company exclaim that what Lawrence III is doing is sick and disgusting. Lawrence III replies that he is a Pokémon collector and now must capture Articuno. Lawrence III goes back to the top of his ship in his seat/elevator.

Ash tries to rescue Moltres by running into the electric rings, but that doesn't work. He then takes out all of his Pokémon to battle the rings. Team Rocket also helps Ash. After much work, the rings finally break apart. Moltres, after experiencing his freedom, uses his fire Zapdos' cage. Zapdos is now free. The 2 Titan birds blow a hole in the wall and escape.

Lawrence III is capturing Articuno at the time by shooting large fire balls at his island. Articuno attacks the ship, and Lawrence III doesn't have time to send rings out. All three birds begin to destroy all of the propellors on the ship, then destroying the ship itself. After much destruction has happened, all three birds battle each other. The ship falls down into the Lightning Island. Ash and all of the gang run down the side of the ship into the snow in front of the shrine. Parts of the boat land on the Lightning Shrine, but the ball rolls out. Ash pockets the ball and goes in a boat that fell in the water from the Air Ship. The boat, with everyone in it, including Team Rocket, speed off to the main island. They cut through the ice, barely escaping the battle of the three Titan Birds. Suddenly a water cyclone pops out of the water. The water cyclone turns in Lugia and blasts the boat all the way to a Ancient Shrine on the main island. Melody notices that Lugia makes the noise that her flute makes. Lugia battles the three birds.

As Ash comes onto the main shrine, Slow King appears and tells Ash to put the treasures, the three balls, onto a Magical Shrine. Ash does so, but to his dismay, he only has two of the balls. Ash doesn't know what to do but to watch the three birds battle. He also notices scores of Pokémon that are just standing around watching. Lugia, the guardian Pokémon, is fighting all three birds at once. The birds are too much for Lugia, and it falls into the ocean. Melody doesn't know what to do so she plays her flute. The song of Lugia, played on the flute, has magical powers, which revives Lugia.

Lugia explains to Ash that somebody must get the third mystic ball, the Ice Ball. It retells the ancient legend and says that the world is doomed. Ash notices that in the ancient legend the last words are 'the world will end and lay in Ash'. Lugia explains that all of the Pokémon have gathered there because they do not know what to do. The Pokémon think that one of them will have the chance to save the world. But only one is the Chosen One. Ash confirms that the 'ash' in the legend is him, and he is the chosen one to take the quest to get the last ball. Everybody around Ash supports him and says that he must. Ash begins to walk in the snow, truding very slowly. Ash spots the broken ship and takes a bent metal slate. He uses the slate as a sled, and using Charizard to tow the sled. The three birds attack Ash. Charizard deflects Moltres' fire and Pikachu wards of Zapdos' lightning attack. Atricuno blasts a wall of ice in front of Ash to interrupt his quest.

Oak, Ivy, and Dodria are in a helicopter in the middle of the Titan Bird battles. They crash right behind the main shrine where Misty, Tracey, the boat driver, and Melody are. Team Rocket, in an inflatable boat they found attack the helicoptor propellor to the back of their craft. Team Rocket zooms toward Ash who is stuck behind the wall of ice. Ash spots Team Rocket and says he doesn't have time to battle. Team Rocket decide to be the good guys this time and help Ash. The hoover craft which Team Rocket made zooms over the ice wall and on to Ice Island. They spot the shrine entrance and fly up the stairs. They get to the Ice Shrine where Ash obtains the Ice Ball.

Articuno flies down from above and crashes into the Shrine just as Ash walks away. Articuno faints on the snow next to the shrine. Lugia tells Ash to get on his back for a swift ride back to the Main Shrine. Team Rocket hops onto Lugia's leg. Team Rocket decides that they are too heavy for Lugia and is only lagging him down. Team Rocket drop in to the ice water below, hoping that what they did will save the world. Lawrence III sends rings to capture Lugia with Ash on him. Lugia, being hurt from the constant attacks from Zapdos and Moltres, who are now fainted, sends massive hyper beams toward the Air Ship which totally destroys it. The rings also dissipate from Lugia's hyper beam. Lugia exclaims that he has failed as he falls into the abyss of water below him. Ash manages to get off Lugia in time and is surfacing over water. Torandoes and lighting storms surroud Ash.

Melody notices what has happened to Ash and she begins to dive into the water. Misty stops her and says that she will go and save Ash. Misty dives into the frigid water and pulls Ash in to the shore. Ash revives from his hypothermia, frostbite, and not being able to breathe. He walks up to the shrine himself, neglecting any assistance from anyone. He puts the Ice Ball into the Main Shrine. Melody, not knowing what to do, plays the Lugia song in an attempt to save the world. Green ooze then comes out of the main shrine and spreads all over the world, fixing everything that has been harmed by the bird's destruction. All the Titan Birds, including the guardian Lugia, are revived. After the water is warm again and the sky is blue, Melody stops playing her ocarina. Everything has now been cured.

Deelia hops down from the crashed helicoptor and says that Ash is in big trouble because he worried her. She explains that Ash is the most treasured thing in her heart. She wishes Ash wouldn't get himself into such danger, but she cannot stop him.

Lugia resurfaces from the water and gives Ash a ride around the archapeligo. A big mettalic rainbow appears overhead. Lugia thanks Ash and tells him to look out upon what he has done. Lugia's final words are, "The Beast of the Sea is now tamed."

Lawrence III says that all that has occured was started because of the tablet's prophecy, the Mew Card.